about

Kandel Group Image Gallery

Welcome to the online image database of the Kandel research group, in the Department of Chemistry and Biochemistry at the University of Notre Dame.

We use Scanning Tunneling Microscopy (STM) to investigate the physical properties and chemical reactivity of surfaces:

  • We have interfaced an in situ STM to a molecular-beam source to investigate gas-surface collision dynamics at the molecular scale. With this apparatus, we can determine how molecular reactivity is controlled by local surface environment and structure.
  • We prepare and characterize monolayers and mixed monolayers of a variety of molecular species (including fullerenes and alkanethiols) on metal surfaces.
  • We study the structural and electronic properties of large, organometallic molecules to determine their suitability as components for molecular electronic devices.

The 18738 images in this database are the results of experiments conducted from September 2001 through February 2006. We are making this database publicly available in the hopes that these images will be useful. If you would like to post, present, or publish one of these images, please read the citation guide below.

S. Alex Kandel, skandel@nd.edu

Details

To manage the gallery, we use zoph, a free online photo album application written in PHP and MySQL. Zoph's extensive search capabilities and simple structure are very well suited to organizing scientific data.

Images are indexed by albums and people; that is, by the instrument on which they are recorded and the student or post-doc who acquired them. Image meta-data is fully searchable: for example, I can search for "image acquired by Daniel Fogarty" and "comment like octanethiol" or "sample bias (V) < 0.1" and "current (nA) > 1.0".

We use commericial software by RHK Technology and Omicron Nanotechnology to acquire STM images in our lab. We have written programs and scripts to parse the microscope files, extract images (as TIFF files) and meta-data, and upload them into zoph. These, along with the modifications we have made to zoph, are available here.

Citation guide

The Kandel group and the University of Notre Dame retain all copyright and other rights for all images in this gallery.

You may use, copy, modify, and link to any image here. If you present or otherwise disseminate our images in an academic or professional setting, please cite us:

  • For informal presentations (in a classroom setting or student seminar) please use the image author's name and mine, our affiliation, and the URL; for example, D. Fogarty and S. A. Kandel, University of Notre Dame, http://graphite.chem.nd.edu/html/kgig
  • For formal presentations (conference presentations or written manuscripts) please contact me so that I can supply a full author list (zoph will only list one author) or, when appropriate, a journal citation.
We upload every image we acquire, good or bad, and images are either unprocessed or batch processed for easy display. Comment fields and some instrument parameters (in particular, tunneling current) are filled in at the time of acquisition (not upload) and may not be correct in all cases. Older images may be misattributed, particularly when students have graduated from the lab (Erin Carmichael, Meaghan Blake, and Phil Nagel). If you have questions about a specific image, or would like to work with the raw data, let us know.

Source code

Download everything here.

We tried to modify zoph as little as possible to create the gallery. We used zoph's translation capabilities to repurpose photographic terms to scientific ones: focal length and distance, for example, become sample bias and tunneling current. In addition, we added several fields to the search menu, and made small changes to the import script. The "zod" (zoph organizes data) "language" and our copies of util.inc.php and zophImport.pl are available on the download page.

Our image file parser is written in C, and can read two types of files from RHK and one from Omicron. It will use file extensions (.SM2, .SM3, or .par) to determine file type, though this can also be specified from the command line. It adjusts image contrast (through a "z exclude" value), subtracts a "best-fit" plane, and has options to do limited high- and low-pass filtering. It saves images as grayscale TIFFs and produces a text file (extension .z) containing experimental parameters, comments, and other data. This file is designed to have the same output format as jhead, which is what zoph uses to parse EXIF data for "real" photos.

We've also included the Perl scripts we use to make batch processing of files a little easier.

Notes

If you find this gallery useful, e-mail me and let me know. If you have fixes or improvements, I'd be interested to hear about them, too.

I'm currently working on modifying stm_to_zoph to output JPEGs with experimental data loaded into EXIF fields, which will make the whole process easier and open up new possibilities for cataloguing images. This is 90% done (see this example) and I will post code when I'm more or less happy with it.